


The TARDIS Knows Best

by Sherlock1110



Category: Doctor Who
Genre: BDSM, Dom Jack, Dom/sub, Handcuffs, Kneeling, M/M, Restraints, Spanking, Sub Tenth Doctor
Language: English
Status: In-Progress
Published: 2016-10-05
Updated: 2017-10-07
Packaged: 2018-08-19 15:06:33
Rating: Mature
Warnings: No Archive Warnings Apply
Chapters: 4
Words: 4,386
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/8213536
Author URL: https://archiveofourown.org/users/Sherlock1110/pseuds/Sherlock1110
Summary: Sherlockian4evr and I have embarked on a Tenth Doctor/Jack Harkness BDSM challenge. We hope to update monthly and have already taken wildly different directions with our fics. Enjoy.





	1. Chapter 1

**Author's Note:**

  * Inspired by [In This Where, When](https://archiveofourown.org/works/8213077) by [sherlockian4evr](https://archiveofourown.org/users/sherlockian4evr/pseuds/sherlockian4evr). 



> Beta read by sherlockian4evr

Jack was grinning like a loon when he entered the hub. The rest of the team had left, gone where they went when they they weren't with him.

He sighed as he looked around; the hub was his. All his. All up until he spotted a particular blue box inside his office.

"Bollocks," he hissed. He grabbed his coat he'd just dumped on the couch and raced up the stairs.

"Doc," he smiled at the Time Lord in his chair.

The Doctor smiled back, but it faltered.

"Captain," he countered.

Jack sighed. He stepped into the room properly and glanced at the box. "Explosion?"

"You can tell?"

"She speaks to me," Jack collapsed in the seat the other side of his desk.

The Doctor dropped his feet down and rested his hands on the table. In seconds his head was pressed into them.

"Depends on your point of view." His face was pressed into the desk, but Jack heard every word.

The captain's head went back to the head rest of the seat. It was several moments before he opened his mouth.

"What have you done?"

He got no response and that was when he realised it was really bad.

Jack stood up and leant over the table. "Doc, what did you do?"

There was still no response, at least not a verbal one, suddenly the Time Lord sat up and tried to lash out.

Somehow, Jack had known, despite the unlikiness to do such a thing in his character. He grabbed his fist as it flew.

"Where's Donna?"

"I don't know. With Martha?"

"Martha? You've met up with her again?"

"Sontarons."

"That was you?"

"No. But it should have been."

"I don't understand."

The Doctor stared him in the eye. "You really don't, do you?"

"How about you drop the cheek and answer the question?" Jack's voice had taken on a stern touch and the Time Lord froze. "What is it?" the younger man asked, worried he had put his foot in it.

"That's it, that's what I need." The Doctor felt incredibly stupid. He took a few steps back until he was leaning against the wall, realisation dawning on him. The TARDIS had taken off from the sontaron problem to pick Donna up from her grandad's and it had landed here. Not with Donna. He grabbed the paper Jack had thrown on the desk this morning. "3 months? Blasted TARDIS!"

Jack was blinking stupidly. "Need? What?"

"You." He stepped forward and gripped Jack's shirt in his hands. He pressed his lips against the captain's.

Surprised, Jack let it continue for a moment before pulling free. "What the hell?"

"You, Jack. That's why she brought me here. For you."

The captain frowned, trying to understand what the Time Lord meant. Then his grin from a few minutes before returned. "I thought you didn't do that sort of thing?" He quirked his eyebrow, waiting for a response.

"I don't. Usually. My TARDIS won't take off. It's clear she wants me here. Its just taken me a long time to work out why."

"Long? How long have you been here?"

"About six hours," he replied with a glance at the clock. Not anywhere near as long as he had thought.

"Why does she want you here?" Came the next question. Jack clearly wanted answers.

"Apart from the obvious?" He shrugged. He didn't know either, he didn't like not know by that didn't help matters. He couldn't work out what being with Jack would achieve. "Why don't you ask her?"

Jack inclined his head and looked over his shoulder at the box. To anyone else, even the other four members of his team, talking to a big blue wooden box would seem strange, but to him; "Alright."

"Do you mind?" The Doctor asked tentatively, he knew what a conversation could be like with his box, especially if she got headed into a temper tantrum.

The captain turned back to face him. "Of course not. And if it gets her to shift arse out of my office it's a win win all round, don't you think?" His grin was back as he pushed the door that had been left ajar, open. 

The Doctor smiled back, but it was fake. He sat back in Jack's chair and stared at the ceiling.

***

It was over an hour later that Jack emerged from the box again. His face was impassive as he glanced around his office to see if anything had changed.

As soon as he was out and had closed the door, the TARDIS dematerialised.

"What?" The Doctor jerked upright and frowned at the captain. "Where's she going?" He glared at the now empty space.

"Down into the archives. She wants to recover." It was also out of the way and a maze. The only person who knew them even remotely well was Ianto Jones. He had been assured she wouldn't try to make any sort of contact with her Time Lord. She'd leave him to Jack.

"From what?" The Doctor asked. Yes, his TARDIS was sentient - almost a 'person' - but that was absurd. It wasn't like there were lots of repairs to be done. The exterior and the interior were as well as could be expected for a box that did what it wanted and refused to fix the chameleon circuit.

"You've been giving her a rough ride recently," Jack countered as if it was obvious.

"I have not!"

Growling, clearly pissed off, Jack reached forward, grabbed the Doctor's shirt in his hand and pulled him up to his feet. Using strength that was abnormal for humans he forced him back into his office wall. He did love his evolution over 21st century people.

"The TARDIS as you well know, is sentient, and you also bloody well know that your link with her has an impact when you are in a bad mood!"

The Doctor breathed heavily for a moment, staring into Jack's deep blue eyes.

"You were in there ages. What did she tell you to do?"

The captain took a step back, but didn't release his grip. He quickly got the heel of his boot in the back of the Time Lord's knee and forced him to the floor.

"Apparently she thinks you need someone to answer to. And as she brought you here, that means me."


	2. Chapter 2

The Doctor tried to force his way back to his feet, but Jack was having none of it. He placed his hand on the Time Lord's shoulder and left it there. It served as a calming presence, but also a warning.

"I need you. I don't need bossing around." The Time Lord's temper kept creeping up on him, in a way it had only done once or twice before, but never had he taken it out on a companion, or an old companion.

"Quiet!" Jack held up his finger, his normal chilled personality all over the place with what he and the TARDIS had just discussed. "The TARDIS disagrees." He crouched down in front of him. "Look at yourself! You're all over the place!"

"I am not! I'm fine. The TARDIS is just being over…"

"Over what? Over protective? Over cautious?"

The Doctor sighed. He had no idea what he was going to say, he could just see himself digging a hole with Jack.

"Where is she? Exactly?"

"I don't know."

"Don't lie to me, Jack. How can you even think you possess the brainpower to ever attempt-"

"I said quiet!" Jack barked. His tone brooked no argument. It was nothing but a captain's tone and it was clearly noticed.

This time the Doctor let his head fall, so his chin was nearly resting on his chest.

"Now I do not know where she's gone, that was the idea. I wouldn't tell you if I did and even if you did know, you wouldn't be going anywhere."

"Oh? And why not?" He snarled up, attempting to stand again. He just couldn't let it go.

Jack snagged a set of the weevil clamps from the desk and tugged his wrists behind him, with a hiss they locked together. He held his arms there for a moment longer before letting him go and watching him fight them.

"What the-"

"You won't unpick them, Doctor, they're attuned to Torchwood employees only." That was kind of obvious given the structure of the clamps, the Doctor realised, but he had to try anyway.

The Time Lord sighed. His day was getting worse and worse.

"The TARDIS suggested a relationship in the context of Dominance and Submission for the period of a month and go from there."

"You're serious about this?"

"Damn right I am. Your time machine is in a bad enough mood to bring you here in the first place. To someone who is wrong to the pair of you just because I have experience with this sort of thing. I am going to take you to bed, for which you will sleep-"

His head snapped up to argue yet again. "Jack, I don't-"

"I know. You sleep about as much as I do. But it is going to happen. You're running on empty and it's making your temper and your attitude unbearable. Then tomorrow we are going to read through a contract that the TARDIS is going to create and we will go from there."

"Jack, I'm not one for… sex. It isn't me, I can't-"

"Shh." His voice was more soothing now and he crouched back down in front of him. "She assured me everything that goes down you would be comfortable with. And even then we don't have to do it. It's a case of knowing where to start."

The kneeling man nodded eventually.

"I trust you, Doc, with my life. I'd like to think that works vice versa, but this will be a different kind of trust."

When he received another nod as a reply, Jack pulled the doctor up to his feet and smashed his lips into the Time Lord's, catching him by surprise.

He had to uncuff him, there was no way he could climb down the ladder in through the manhole if he didn't. It would have been stupidly reckless to even try.

When he joined him under his office he ordered him to strip off his clothes, still holding the clamps in his own hand.

Slowly, yet obediently, the Doctor began to strip his clothes off. They were launched in the direction of a nearby chair.

"I'll be getting your clean suits from the TARDIS, you'll have no reason to go in it."

Sadly, the older man nodded, for which Jack was surprised this time. He would have thought that was reason enough to kick up a fuss. Or maybe he had just had enough for the day.

He took him through to the toilet and indicated which door it was behind, then he turned his back. It was too early in the relationship to take that much of a step that could be embarrassing for the Time Lord.

The captain remained as professional as he could as he led the other man back from the toilet and to the bed. He pushed him back down onto it. Glad he still had his own clothes on, hiding his own hardening cock. He pressed his wrists up towards the bars of the headboard and cuffed his hands around it. He was gentle against such pale cold wrists. The man was a freezer, he knew about the lower body heat, but he must surely still get cold.

"You won't be taking off in the night," he pointed out. "Even if you did uncuff yourself, you can't get out of the hub."

The cuffed man looked confused.

"You'll have a job finding a way for a start, then trying to work out the system."

"I'm not an idiot, Jack."

"And the door was first designed with you in mind, remember?" He leant forward and pecked the Doctor on the tip of his nose. "Night."

He stripped off his own clothes, but made sure he had his pants on when he settled in beside him, he didn't want either of them getting ideas. That was for another day.


	3. Chapter 3

When the Doctor awoke the following morning, it was a surprise when he tried to stretch and found himself tied to the bed he was laying on. Before he panicked, he looked around for any signs that would give away where he was. 

There was nothing. Nothing to indicate where he was or what he was doing. He did a mental catalogue of his current state… no injuries, no drugs in his system, just really achey and really tired… and then the entirety of the previous evening came flooding back. 

"Jack!" He yelled, after making sure the Torchwood leader hadn't hidden under the bed or something. He was far calmer now than he had been. He'd been out of it completely, no sense of time or location, that wasn't good to wake up to. 

"Jack!" He tried bellowing this time. 

There was the sound of footsteps above him and then the thud, thud, thud on the ladder. 

"Doc? Doc, are you alright?" 

Jack rushed over and saw that the Time Lord was just fine and he let himself breathe easily. 

"Are you going to untie me?"

Jack's grin at seeing the Time Lord alright disappeared to be replaced by irritation. 

"I think you should ask nicely."

"I think you should get off your high horse."

Jack shrugged and headed back towards the ladder. If the sod wanted to be a brat, then he wouldn't stop him. 

"No, Jack, wait," the Doctor called after him. 

The captain paused on his way to the manhole, but he didn't turn around, just focused his attention on listening. 

"Untie me. Now. I've got things to do."

Jack whirled around on his toe. "You've got nothing to do! Your TARDIS has seen to that. In case you had forgotten, you're my responsibility now."

The Time Lord just glared at him. 

"You're on punishment level 2 already. It's a shame you hadn't waited until after our little chat, isn't it? At least then you'd know what that meant."

"Jack, this is getting tedious."

"So is your attitude. Ask me nicely and I'll uncuff you. You'll be able to get a shower and we can have that chat."

When the Doctor clearly wasn't going to speak anymore, Jack sighed and turned his direction towards the ladder once more. 

This time when he was called after, he didn't stop, he just kept walking to the ladder. Strict and fair, he reminded himself. They were the two main words the TARDIS had told him the day before, they also appeared quite a few times in the contract he had collected a few hours ago. 

Before he left up the ladder, he placed a small listening device on his workout bench, then he ascended and headed out into the hub. The team were wandering in, the kitchen light was on so he knew Ianto was about, Tosh was already at her desk and just as he stepped into the main body of the hub, Owen came racing in being followed by Gwen at speed. She caught him up and tried to yank his trousers down in front of the water feature. 

Jack clapped his hands, gaining their attention before the ex copper could get a chance to succeed in her mission. Owen used the distraction to duck around the water feature and sit in the safe confines of his own desk. 

"Tosh, there was limited activity through the night, do you want to check the new programs are up and running properly?"

"Sure," she smiled up at him, not stopping in her typing at all. 

"Owen, that dead weevil needs seeing to and you have about 15 reports you still need to write, that's without including yesterday's fiasco. Gwen, give Ianto a hand with archiving some of the equipment we picked up yesterday, it'll need the both of you."

"But, Jack, that's Ianto's-"

"No arguments, it needs doing."

Gwen rolled her eyes. "Charming."

"Chop chop, then!" He tapped the metal railing with another bar from a few floors up. "Things to do!" 

With that, he headed back into his office and sighed. The Time Lord still hadn't spoken, clearly choosing to lay there in silence instead. He briefly wondered how he was going to get the Doctor to meet his team. If he was staying a while, then that would need to happen. They were all aware why he had run off last year, with the hand in a jar. They'd want to meet him for that reason and the fact this was Torchwood and he was the Time Lord they were built to protect the Earth from. Things had changed, he only hoped their viewpoint on him changed too. 

It turned out, it was well over two hours later, Jack had eaten breakfast in the boardroom with the rest of the team, not sure how to broach the subject of the alien in the bunker or when. 

He hoped Tosh found out herself and came looking for answers, but so far the rift programs weren't pointing out any faults. So how had the Doctor jumped them? No alarms were blaring when he'd entered the hub the previous night. 

Back in his office, he finally heard the Doctor fighting for his freedom again. 

He headed back down the ladder and folded his arms across his chest in front of the Doctor. 

"Jack, please let me go."

The captain nodded. "It seems a few hours alone works wonders. You never were one for solitude."

Jack deactivated the weevil cuffs and pulled him upright. He couldn't help but brush his hand over the Time Lord's hair in an attempt to soothe him. He found it odd when his new sub didn't try and duck away from it. He smiled down at him before he pulled him to his feet, "Bathroom's through there, your suit is on the side, meet me upstairs when you're done."

***

The Doctor climbed the ladder cautiously, but he couldn't help but grin at the sight of the banana on the desk and an array of other foods. 

"I would usually say I'm not hungry."

"Well you'll be eating regularly here. You don't look after yourself well at the best of times." The captain nodded at the seat the other side of his desk. "Take a seat."

***

Jack waited for the Time Lord to finish eating before speaking to him. He'd already collected the contract drawn up by the TARDIS. 

He watched closely as the Doctor read through it. 

"Have you a problem with any of that?"

"Yes. All of it."

Jack didn't know whether to laugh or cry at that statement. Instead he folded his arms and let out a deep breath. 

"I can start with a level 3 punishment, if you like."

The Time Lord frowned, "No. No, thanks, Jack. I'm fine."

"You need to get this into your head. This is happening. Right here, right now. You aren't going anywhere, so accept your punishment, accept the new role you've found yourself in and maybe things will sort themselves out."

At the knock on the door, Jack looked up, glad for the interruption. "Yeah?"

"Coffee, sir," Ianto said with a grin from the doorway. Then he paused at the sight of the Doctor sat in the chair opposite Jack's desk. His brow furrowed, the man looked mad. 

"Ianto, thanks. This is the Doctor." He took the mug from the archivist and nodded his head in the Time Lord's direction. "We were just having a little chat, weren't we, Doc?"

The Doctor didn't reply, his usual happy bubbly self gone at what the TARDIS had deemed his new life on a piece of paper. 

"You were at Canary Wharf," Ianto spoke eventually when the new man didn't look up.

"And?" He growled, not looking up. "So were thousands of other people!"

"Doctor!" Jack snapped, "I think it best if you went back down into the bunk."

At that, he looked up. "Fine," he grumbled, he kicked the chair back and quite literally stropped off towards the ladder.


	4. Chapter 4

**Notes for the Chapter:**

> A long time, I know...

"What's he doing here, sir?" Ianto asked as he kicked the man hole cover closed. 

"His... ship brought him. He needs my help."

Ianto frowned, was he really going to give that man help? "Didn't he leave you? To fend for yourself? Hundreds of miles away."

Jack sighed. "Years ago, yes. But ive seen him since, he's different now."

"You told me he couldn't physically be near you."

"Slight over exaggeration. I'm fine. He's fine. Well, he's not fine, but he will be."

Ianto nodded once, it was clear Jack wasn't going to speak to him about the situation. "Very well, sir. Is there anything else I can get for you?"

The captain sighed, he knew that look all too well, but there was nothing he could do about it right now. "The Doctor will have a cup of tea when I text you. 3 sugars."

"Of course," Ianto left the office feeling like he hadn't gained anywhere near the information he should have. For some reason, he stopped himself telling the rest of the team of the Time Lord's presence. 

***

Jack climbed down the ladder into the bunker just under an hour later. It had taken him that long to get his head in the correct spot for what he was about to do. 

He sighed heavily when he glanced around his room and noticed it empty. The only way out was through the latch and he hadn't left his office for the Time Lord to sneak out. He must be in the bathroom. As he turned to face it, he saw the bathroom door shut. He didn't need to try it to know it was locked. 

"Doctor, come out of there right now."

There was no response, but the captain hadn't really been expecting one. He had two options here, kick the door in, or pick the lock. 

The lock was cheaper, he smirked as he grabbed his screwdriver set up from the wardrobe and quickly worked it into the lock.. 

As he swung the door open wide he saw the Doctor giving him a death glare from where he had his hands wrapped around his knees in the toilet. 

"Out," Jack ordered. "Now."

When there was still no response, he reached over, grabbed him by the scruff of the neck and yanked him towards the bedroom. 

"On the bed!" He yelled shoving him towards it. 

"Jack, don't you-"

"Now!" The full military side of the captain came flying to the surface and the fire in the Doctor's eyes didn't affect him at all. 

With a sigh, the Doctor sat on the bed. 

"You are a guest here, Doctor. You do not treat my staff the way you just treated Ianto. You will be punished for that."

"What-"

"Enough!" Jack roared. He went to the cupboard and began touring through it. 

Behind him, he heard the Time Lord's footsteps across the room then up the ladder and he didn't even blink. The Doctor whacked the man hole cover with his palm then searched his pockets for his sonic screwdriver. 

When he realised it wasn't there, he glanced down and saw Jack with his arms folded, in one hand was a pair of cuffs. 

"Jack-"

"Down. Now!"

Seeing no way out, he slid down the ladder easily and landed on nimble feet. 

"Here," Jack pointed at the floor in front of him. After several seconds the Doctor was stood in that spot, a rather pissed off look on his face at having been outsmarted by a drain cover. 

"Turn around."

When the Doctor refused to obey that command, Jack stepped around him, grabbed his wrists and threw him up against the nearest wall. He quickly had the cuffs in place, not tight enough to hurt, but enough that the Time Lord couldn't slip them, then he dragged him across the bunker and collapsed on his bed, pulling the Time Lord down over his lap. 

"Jack, what the hell-" the Doctor was already blushing bright red with embarrassment. He was a fully grown man, this couldn't happen!

"You will be getting a spanking, Doctor. I can do it over your trousers or under them. It's entirely your choice."

***

20 minutes later and Jack was delivering the final 10 blows. He had given him 6 blocks of 10, the last of which were given on his bare arse while his trousers were around his ankles. 

"Jack, I'm sorry," the Doctor sobbed. 

Closing his eyes and taking a deep breath in, Jack pulled him up on his lap and wrapped his arms around him. He ignored the Doctor's limp cock, he hadn't been aroused by that at all which was good. 

"When we go back upstairs you'll apologise to Ianto. Are we clear?"

The Doctor nodded, turning his head into Jack's neck and hiding his bright red face. 

The Torchwood captain held him for a long while. Long enough that the younger man fell asleep where he was curled. Jack relaxed back against the unit and held him tight. He was lucky he had a higher pain threshold than normal humans, or his hand would be throbbing rather than just being red. It matched the Time Lord's ass perfectly. He smiled down at it, surprised he wasn't completely rock hard in his pants. 

Instead, he found his attention drifting, he was still going over everything the TARDIS had told him, how far he would have to go to get a reaction out of the Time Lord compared to his previous submissives. It would be different. Very different. 

It had only been 3 blocks of 10 before with subs when he'd been younger. But after 30 swats, the Doctor had hardly flinched. He would need to get a better understanding of the way Time Lord physiology differed from humans and how he could punish him in the future. 

But not only to punish him, but to find out how best to reward him as well. That's what he wanted more than anything, to reward the man rather than punish him. He just wanted to treat him right.


End file.
